I have been working on my population genetics project. One of the main thing is to plot the data in the context of the sampling locations. I have been searching all different kinds of solutions. One of the best for my application was to use the packages: maps, mapplots.

I didn't find it difficult to install or compile the egglib module on Linux, when I first come to use egglib in python. However, things changed my mind when I was trying to use the internal function Align.polymorphismBPP(), which is a function that depends on the Bio++ library supoort. Somehow, I didn't install the C++ module correctly in the beginning, thus now I need to pay the price.

Before we get into the installation, we need to make sure the pre-requisites by egglib and my local platform configuration.

A python script writen in OOP style to simulate population genetic dfrit and spontaneous mutation. Microsatellite markers were used as a surrogate to calculate genetic diversity across time/generations.

A friend of mine is going to set up a plant pathology lab soon, and he is planning working with some bioinformatics work over there. I am helping him build a lab server with a reasonable price, which in this case was USD1.5k. I plan to use this opportunity to write a blog to document the whole process to share with the potential community.

Nowadays, next generation sequencing (NGS) is becoming affordable and approachable to most of the labs. Although many other options are out there for people who want to seek for data computing solutions. But the cheap way for a lab with limited fundings could be a lab-owned server. Now let’s see what we can get with this price, and what’s the performance is gonna be.